Hi Corinna, are you sure that the mri-in-hardi.nii.reg registration is
accurate? the following should look in register:
tkregister2 --reg mri-in-hardi.nii.reg --mov mri-in-hardi.nii --surfs
doug
On 03/25/2013 06:09 PM, Corinna Bauer wrote:
I am trying to get the V1 label to map onto my HARDI
Hello all,
I am attempting to run bbregister on 4D HARDI data that has already been
motion, eddy, and epi-distortion corrected in fsl. I run the command:
bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti
--init-fsl --reg register.dat and get a number of errors that seem to
Hi Corinna, can you run
fslregister --debug --s lindsay --mov
hardi/ffiltered_func_data_01.nii.gz --reg fsl.reg.dat --niters 1
--maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol
brainmask | tee dng.log
and send me the dng.log?
doug
On 03/25/2013 12:39 PM, Corinna Bauer
Can you verify that
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/brainmask.mgz
exists?
doug
On 03/25/2013 12:55 PM, Corinna Bauer wrote:
sure. Here is the dng.log.
Corinna
On Mon, Mar 25, 2013 at 12:45 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
yes, this file exists.
On Mon, Mar 25, 2013 at 1:10 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Can you verify that
/usr/local/freesurfer/**subjects/symmetry/lindsay/mri/**brainmask.mgz
exists?
doug
On 03/25/2013 12:55 PM, Corinna Bauer wrote:
sure. Here is the dng.log.
Corinna, can you edit $FREESURFER_HOME/bin/bbregister? If so, change the
following line
From
set cmd = (fslregister --s $subject --mov $regvol --reg $InitReg \
--niters 1 --maxangle 90 --tmp $tmpdir/fslregister \
--dof $FSLDOF --fsvol $fsvol)
To
set cmd = (fslregister --s
Ok I adjusted the bbregister file to say fsvol.mgz in the location you
specified and got this error a bit later on in the bbregister output:
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/symmetry
cd /usr/local/freesurfer/subjects/symmetry/lindsay
/usr/local/freesurfer/bin/bbregister --s
Are you sure you made the right edit? It should be --fsvol $fsvol.mgz
It looks like you might have changed it to --fsvol.mgz $fsvol
On 03/25/2013 01:30 PM, Corinna Bauer wrote:
Ok I adjusted the bbregister file to say fsvol.mgz in the location you
specified and got this error a bit later on
yep, looks right
On 03/25/2013 03:12 PM, Corinna Bauer wrote:
Also, I now want to apply the inverse transform to move the T1 into
the HARDI space. Did I do this correctly? It looks good in tkregister.
mri_vol2vol --mov hardi/ffiltered_func_data_01.nii.gz --targ
mri/orig.mgz --reg
